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- PDB-8xx4: ASFV RNAP elongation complex -

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Basic information

Entry
Database: PDB / ID: 8xx4
TitleASFV RNAP elongation complex
Components
  • (DNA-directed RNA polymerase ...) x 5
  • C122R
  • D339L
  • DNA (5'-D(P*CP*GP*CP*AP*AP*CP*GP*GP*CP*GP*A)-3')
  • DNA (5'-D(P*TP*TP*CP*GP*CP*CP*GP*TP*TP*GP*CP*GP*TP*AP*TP*TP*TP*GP*TP*GP*TP*AP*G)-3')
  • RNA (5'-R(P*CP*UP*AP*CP*AP*CP*AP*AP*A)-3')
  • RNA polymerase subunit 6
KeywordsTRANSCRIPTION/RNA/DNA / ASFV / RNAP / elongation complex / TRANSCRIPTION-RNA-DNA complex
Function / homology
Function and homology information


viral transcription / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / virion component / : / : / : ...viral transcription / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / virion component / : / : / : / : / : / : / DNA-directed RNA polymerase / host cell cytoplasm / protein dimerization activity / DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. ...RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / C122R / DNA-directed RNA polymerase RPB5 homolog / RNA polymerase subunit 6 / DNA-directed RNA polymerase RPB10 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase RPB3-11 homolog / D339L / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhu, G.L. / Zhu, Y. / Zhu, Z.X. / Sun, F. / Zheng, H.X.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFD1800105 China
Ministry of Science and Technology (MoST, China)2021YFD1801300 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of RNA polymerase complexes in African swine fever virus.
Authors: Guoliang Zhu / Fei Xi / Wuxia Zeng / Yifei Zhao / Weijun Cao / Chen Liu / Fan Yang / Yi Ru / Shuqi Xiao / Shilei Zhang / Huanan Liu / Hong Tian / Fayu Yang / Biao Lu / Shukai Sun / Haiyang ...Authors: Guoliang Zhu / Fei Xi / Wuxia Zeng / Yifei Zhao / Weijun Cao / Chen Liu / Fan Yang / Yi Ru / Shuqi Xiao / Shilei Zhang / Huanan Liu / Hong Tian / Fayu Yang / Biao Lu / Shukai Sun / Haiyang Song / Bozhang Sun / Xiaoyi Zhao / Lijie Tang / Kangli Li / Jijun He / Jianhong Guo / Yun Zhu / Zixiang Zhu / Fei Sun / Haixue Zheng /
Abstract: African swine fever virus is highly contagious and causes a fatal infectious disease in pigs, resulting in a significant global impact on pork supply. The African swine fever virus RNA polymerase ...African swine fever virus is highly contagious and causes a fatal infectious disease in pigs, resulting in a significant global impact on pork supply. The African swine fever virus RNA polymerase serves as a crucial multifunctional protein complex responsible for genome transcription and regulation. Therefore, it is essential to investigate its structural and functional characteristics for the prevention and control of African swine fever. Here, we determine the structures of endogenous African swine fever virus RNA polymerase in both nucleic acid-free and elongation states. The African swine fever virus RNA polymerase shares similarities with the core of typical RNA polymerases, but possesses a distinct subunit M1249L. Notably, the dynamic binding mode of M1249L with RNA polymerase, along with the C-terminal tail insertion of M1249L in the active center of DNA-RNA scaffold binding, suggests the potential of M1249L to regulate RNA polymerase activity within cells. These results are important for understanding the transcription cycle of the African swine fever virus and for developing antiviral strategies.
History
DepositionJan 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase RPB3-11 homolog
D: DNA-directed RNA polymerase RPB5 homolog
F: D339L
G: C122R
H: DNA-directed RNA polymerase RPB10 homolog
P: RNA (5'-R(P*CP*UP*AP*CP*AP*CP*AP*AP*A)-3')
T: DNA (5'-D(P*TP*TP*CP*GP*CP*CP*GP*TP*TP*GP*CP*GP*TP*AP*TP*TP*TP*GP*TP*GP*TP*AP*G)-3')
E: RNA polymerase subunit 6
N: DNA (5'-D(P*CP*GP*CP*AP*AP*CP*GP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,74618
Polymers422,33011
Non-polymers4177
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA-directed RNA polymerase ... , 5 types, 5 molecules ABCDH

#1: Protein DNA-directed RNA polymerase subunit / ARPB1


Mass: 162959.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus
References: UniProt: A0A3S7XUW7, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / ARPB2


Mass: 138989.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus
References: UniProt: A0A2X0RU95, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase RPB3-11 homolog / ARPB3


Mass: 41286.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A2X0RUE7
#4: Protein DNA-directed RNA polymerase RPB5 homolog / ARPB5


Mass: 23693.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0A1E0C1
#7: Protein DNA-directed RNA polymerase RPB10 homolog / ARPB10


Mass: 9098.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0A1E360

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Protein , 3 types, 3 molecules FGE

#5: Protein D339L / ARPB7 / D339L CDS protein / D339L protein / Protein D339L


Mass: 9200.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A2X0RV08
#6: Protein C122R / ARPB9 / C122R CDS protein / C122R protein / PC105R / PC122R


Mass: 11617.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0A1DYD1
#10: Protein RNA polymerase subunit 6 / ARPB6


Mass: 12207.306 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0A1E0Q7

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RNA chain , 1 types, 1 molecules P

#8: RNA chain RNA (5'-R(P*CP*UP*AP*CP*AP*CP*AP*AP*A)-3')


Mass: 2822.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus

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DNA chain , 2 types, 2 molecules TN

#9: DNA chain DNA (5'-D(P*TP*TP*CP*GP*CP*CP*GP*TP*TP*GP*CP*GP*TP*AP*TP*TP*TP*GP*TP*GP*TP*AP*G)-3')


Mass: 7084.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus
#11: DNA chain DNA (5'-D(P*CP*GP*CP*AP*AP*CP*GP*GP*CP*GP*A)-3')


Mass: 3368.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus

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Non-polymers , 2 types, 7 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ASFV RNAP elongation complex / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: African swine fever virus
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73192 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429579
ELECTRON MICROSCOPYf_angle_d0.5740214
ELECTRON MICROSCOPYf_dihedral_angle_d10.5314269
ELECTRON MICROSCOPYf_chiral_restr0.0454567
ELECTRON MICROSCOPYf_plane_restr0.0055028

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